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Standard Name	yniC
Gene Synonym(s)	ECK1725, b1727, JW1716^[1], JW1716
Product Desc.	2-deoxyglucose-6-phosphatase^[2]^[3] 2-deoxyglucose-6-P phosphatase; mutants are hypersensitive to 2-deoxyglucose; overproduction confers 2-deoxyglucose resistance; additional in vitro substrates: mannose-6-P phosphate, 2-deoxyribose-5-P, ribose-5-P, glucose-6-P; HAD1^[4]
Product Synonyms(s)	predicted hydrolase^[1], YniC^[2]^[1], B1727^[2]^[1] , ECK1725, JW1716, b1727
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yniC^[2]
Regulation/Activity
Quick Links
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Notes

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In vitro activities and phenotypes demonstrated by Kuznetsova et al. (2005, 2006). HAD superfamily. HT_Cmplx36_Cyt: Mog+YniC.^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	yniC
Mnemonic	Systematic nomenclature
Synonyms	ECK1725, b1727, JW1716^[1], JW1716
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	38.96 minutes	MG1655: 1807404..1808072 <gbrowseImage> name=NC_000913:1807404..1808072 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1786645..1787313 <gbrowseImage> name=NC_012967:1786645..1787313 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1699463..1700131 <gbrowseImage> name=NC_012759:1699463..1700131 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1811094..1811762 <gbrowseImage> name=NC_007779:1811094..1811762 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1897975..1898643 <gbrowseImage> name=NC_010473:1897975..1898643 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability
ΔyniC (Keio:JW1716)	deletion	deletion			PMID:16738554	Shigen CGSC9449^[5]
ΔyniC::kan	deletion		Biolog:respiration	unable to respire N-Acetyl-D-glucosamine	PMID:16095938
ΔyniC::kan	deletion		Biolog:respiration	unable to respire a-D-Glucose-6-phosphate	PMID:16095938
ΔyniC::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔyniC::kan	deletion		Biolog:respiration	unable to respire a-Ketobutyrate	PMID:16095938
ΔyniC726::kan					PMID:16738554	CGSC:105834
not named in paper		D13A, D15A		Mutation of predicted catalytic residues results in loss of >99.9% of the phosphatase activity.	PMID:16990279
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW1716	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCAACCCCGCGTCAGATTCT Primer 2:CCACCGAGAAGGTCTTTTGCGGT
8A4	Kohara Phage	Genobase	PMID:3038334
19B6	Kohara Phage	Genobase	PMID:3038334
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[5]	est. P1 cotransduction: 30% ^[6] Synonyms:zdh-925::Tn10
zdj-276::Tn10	Linked marker	CAG18464 = CGSC7387^[5]	est. P1 cotransduction: 39% ^[6] Synonyms:zdi-276::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:G6932	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13988	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003520	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945632	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3744	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005761	Escherichia coli str. K-12 substr. MG1655
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Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	YniC
Synonyms	predicted hydrolase^[1], YniC^[2]^[1], B1727^[2]^[1] , ECK1725, JW1716, b1727
Product description	2-deoxyglucose-6-phosphatase^[2]^[3] 2-deoxyglucose-6-P phosphatase; mutants are hypersensitive to 2-deoxyglucose; overproduction confers 2-deoxyglucose resistance; additional in vitro substrates: mannose-6-P phosphate, 2-deoxyribose-5-P, ribose-5-P, glucose-6-P; HAD1^[4]
EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0004346	glucose-6-phosphatase activity	PMID:16990279	IDA: Inferred from Direct Assay		F	Figure 1. Note that activity on glucose-6-P was lower than other substrates tested.	complete
	GO:0050308	sugar-phosphatase activity	PMID:16990279	IDA: Inferred from Direct Assay		F		complete
	GO:0003850	2-deoxyglucose-6-phosphatase activity	PMID:16990279	IDA: Inferred from Direct Assay		F	Figure 1.	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005834	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003850	2-deoxyglucose-6-phosphatase activity	PMID:16990279	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0004346	glucose-6-phosphatase activity	PMID:16990279	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005833	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005834	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	PMID:16990279	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016791	phosphatase activity	PMID:16990279	IDA: Inferred from Direct Assay		F	YniC had phosphatase activity on 11 of 80 phosphorylated compounds tested (listed in order of decreasing activity): 2-deoxy-glucose-6-P, erythrose-4-P, mannose-6-P, 3-phosphoglyceraldehyde, 2-dedoxyribose-5-P, glucose-6-P, ribose-5-P, glucosamine-6-P, fructose-6-P, fructose-1-P, and FMN.	complete
	GO:0046872	metal ion binding	PMID:16990279	IDA: Inferred from Direct Assay		F	Binds to Mg2+, Mn2+, Co2+, and Zn2+ (Suppl. Table 2). Km varies depending upon substrate present.	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	uidC	PMID:16606699	Experiment(s):EBI-1140627
Protein	rplJ	PMID:16606699	Experiment(s):EBI-1140627
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MSTPRQILAA IFDMDGLLID SEPLWDRAEL DVMASLGVDI SRRNELPDTL GLRIDMVVDL WYARQPWNGP SRQEVVERVI ARAISLVEET RPLLPGVREA VALCKEQGLL VGLASASPLH MLEKVLTMFD LRDSFDALAS AEKLPYSKPH PQVYLDCAAK LGVDPLTCVA LEDSVNGMIA SKAARMRSIV VPAPEAQNDP RFVLADVKLS SLTELTAKDL LG
Length	222
Mol. Wt	24.33 kDa
pI	4.7 (calculated)
Extinction coefficient	20,970 - 21,345 (calc based on 3 Y, 3 W, and 3 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Domain	7..185	PF00702 haloacid dehalogenase-like hydrolase		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=yniC taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16129681	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945632	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005761	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77247	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6932	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13988	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945632	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003520	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3744	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MC4100	2.95E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	1568	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	525	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	982	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
yniC
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:1807384..1807424 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b1727 (EcoliWiki Page)	NCBI GEO profiles for yniC
microarray	GenExpDB:b1727 (EcoliWiki Page)	Summary of data for yniC from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (1806957..1807225) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ10; Well:F7^[7]
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Notes

Accessions Related to yniC Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:G6932	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3744	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1727
EcoGene	EcoGene:EG13988	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003520	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005761	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Arabidopsis thaliana	AT1G56500 (score: 1.000; bootstrap: 78%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00042333 (score: 1.000; bootstrap: 100%) WBGene00023956 (score: 0.787)	From Inparanoid:20070104
Shigella flexneri	YNIC	From SHIGELLACYC
E. coli O157	Z2756	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00702 haloacid dehalogenase-like hydrolase
Superfamily (EcoliWiki Page)	SUPERFAMILY:56784
EcoCyc	EcoCyc:G6932	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13988	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003520	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3744	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005761	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yniC:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

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Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to yniC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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